One
of the earliest published reports concerned DNA extracted from fossil Magnolia
leaves (with intact fragments measuring up to 800 base pairs) found in lake
bottom sediments of Miocene age, supposedly 17-20 million years old.3 This
find was quite interesting because the magnolia leaves were still wet. Of
course, DNA disintegrates fairly rapidly when in contact with water. In
commenting on the remarkably old DNA in the supposedly 17-million-year-old
magnolia leaf, Savante Pääbo
exclaimed, "The clay was wet, however, and one wonders how DNA could have
survived the damaging influence of water for so long." 24

However,
most of the DNA which has been recovered is from insects and plants preserved in
dry amber, including a termite estimated to be 25-30 million years old,2
a Hymenaea leaf thought to be 25-40 million years old5 and a weevil
estimated to be 120-135 million years old.1 The weevil DNA is
currently claimed to be 80 million years older than any other fossil
DNA ever extracted and sequenced.

Even more amazing than this though are the findings of Dr. Cano, a
microbiologist at California State Polytechnic University. What Dr. Cano
did was dissect a Dominican stingless bee trapped in amber, which was thought to
be 25 to 40 million years old. What he found were very well preserved
bacterial spores inside. In fact they were so well preserved that they
actually grew when placed in the right environment. In other words, they
were still alive! And, interestingly enough, their DNA closely matched the
DNA of modern bacteria that grow inside modern bees. 26 Also, fairly
recently, a viable bacterium was isolated from a primary salt crystal dated at
over 250 million years old. 30

However,
although DNA extracted from amber was maintained in a fairly dry environment,
these findings of extremely "ancient" DNA in amber are still
problematic.R.
John Parkes commented in a fairly recent issue of Nature concerning this
and other similar phenomena by noting that, "There is also the question of
how bacterial biopolymers can remain intact over millions of years in dormant
bacteria; or, conversely, if bacteria are metabolically active enough to repair
biopolymers, this raises the question of what energy source could last over such
a long period." 29

Such
discoveries have been widely reported by the media. But what has been largely
ignored is the difficulty that these finds present for the standard geological
time scale.

DNA, like all other biological macromolecules, is clearly quite unstable, and
spontaneously breaks down - especially when hydrated or "wet". In
living cells, DNA is maintained by repair mechanisms, but after death DNA
self-destructs at a rather rapid rate.In
a recently published review of the chemical stability of DNA, Tomas Lindahl
(1993) has said, “deprived of the repair mechanisms provided in living cells,
fully hydrated DNA is spontaneously degraded to short fragments over a time
period of several thousand years at moderate temperatures”.

Lindahl went on to argue for the "contamination" of all such
specimens by modern DNA suggesting that, "The apparent observation that
fully hydrated plant DNA might be retained in high-molecular mass form for 20
million years is incompatible with the known properties of chemical structure of
DNA." 28 In a 1991 issue of Science Jeremy Cherfas
expressed his bewilderment noting, "That DNA could survive for such a
staggering length of time was totally unexpected - almost unbelievable." 25

In
a similar vein, Sykes (1991) has commented that in vitro estimates of the rate
of spontaneous hydrolysis imply that no DNA would remain intact much beyond
10,000 years. In his review paper, Lindahl goes on to argue that “it seems
feasible that useful DNA sequences tens of thousands of years old could be
recovered, particularly if the fossil has been retained at low temperature,”
giving as an example DNA from mammoth tissue thought to be 40,000 years old. So,
our knowledge of DNA stability makes it seem highly improbable that this
molecule could be preserved for more than a few tens of thousands of years at
most.

Others have noted that, "Certain physical limits seem inescapable.
In approximately 50,000 years, water alone strips bases from the DNA and leads
to the breakage of strands into pieces so small that no information can be
retrieved from them. Oxygen also contributes to the destruction of DNA. Even in
ideal conditions–in the absence of water and oxygen and at low
temperature–background radiation must finally erase all genetic
information," 27

Yet,
the fossils from which DNA has been recovered are thought to be, in some cases,
tens of millions of years old.There
is obviously a problem here.It is
for this reason that some scientists are now viewing some of the reported finds
(especially those that do not involve preservation in amber) skeptically.It has been argued that some of the detected residues were the result of
contamination by modern DNA, so more recent workers have been conscientious in
arguing that they have eliminated this possibility. In any case, the data, as
presently known, does not sit comfortably with the accepted millions of years
time scale.

Very
Old Protein

Despite
the reproducible evidence that DNA as well as many proteins are rather unstable
and decay relatively rapidly, the positive reported findings of such existent
material in fossils supposedly millions of years old, seems rather intriguing.For example:In 1992, Dr. Muyzer,
et al., used polymerase chain
reaction (PCR) to amplify a protein that they suspected to be osteocalcin from
two Cretaceous dinosaurs identified as “Lambeosaurus F38” (which they
believe to be 75.5 million years old), “Pachyrhinosaurus F39” (supposedly
73.25 millions years old), and a third dinosaur sample identified only as
“F33”. They used two different methods to determine if this protein really
was osteocalcin or not.

The
first method used an immunological reaction. Here is how it works:When a few molecules of a foreign substance are injected into an animal,
that animal’s immune system will naturally produce antibodies to fight it. The
kind of antibodies it produces depends on the kind of foreign material
introduced. Furthermore, the animal’s immune system will produce lots of
antibody cells in response to just a few foreign molecules, so the antibodies
are much easier to detect than the foreign material itself.

The
researchers took some osteocalcin from alligator bones and injected it into a
rabbit to see what kind of antibodies the rabbit produced to fight off the
osteocalcin. Then they took some powdered dinosaur bones and injected it into
the rabbit, and it produced the same kind of antibodies, indirectly indicating
that there was osteocalcin in the powdered dinosaur bones. The second method
used a direct measurement of Gla/Glu ratios “detected by high-performance
chromatography.” 7

Their
conclusion was that both methods showed osteocalcin was still present in the
three different dinosaur bones they analyzed. This was published in October,
1992. The literature search found that all the articles on organic material
still present in dinosaur bones were published from April 1990 until November
1994 (As far as I can tell, there has been nothing published in Nature
or Science on the subject since
then). In the same publication as Dr. Muyzer 7, Dr. Matthew Collins
made the following statement:

"Dinosaurs
hold an enduring fascination. We reported the detection of a protein in a
dinosaur bone, published at around the same time as the release of Steven
Spielberg's blockbuster, Jurassic Park, [so it] was bound to receive the
full media treatment. Our report claimed to have detected osteocalcin
immunologically and also to have found an unusual amino acid g-carboxyglutamic
acid (Gla) in a dinosaur bone from immature (unheated) sediments.
Osteocalcin is peculiarly suited to such spectacular survival, it is very
abundant in bone, binds strongly to it and has the distinction of being the
only ancient protein ever to have been sequenced."

Some
articles suggested that the finding had brought forward the chances of
successfully turning the science fiction of Jurassic Park into scientific fact. Elsevier
magazine (2/10/93) stated "[The detection of osteocalcin] has set other
scientists thinking, if it is possible for a protein, perhaps it is also
possible for DNA". The Daily
Telegraph even suggested that trend-setting restaurateurs may start serving
dinosaur soup! The scientific community was more skeptical.Jeff Bada (an experienced protein geochemist) warned in a 1992 interview
in Science News "I worry greatly
about the stability of Gla.Why
would it remain unaltered for tens of millions of years?".

Scientists
are asking, "How can this protein be so fresh when it is contained in such
old bones?" We should consider the possibility that they will never find
the answer because they might be asking the wrong question. Maybe they should
ask, "How can these bones be so old when they contain such fresh
protein?" That throws a whole new light on the subject. They will not ever
figure out how protein and DNA can last for tens of millions of years without
breaking down if protein and DNA cannot really last for tens of millions of
years. They might just as well be wasting their time.

Really
"Old" Dinosaur Soft Tissues, Blood Cells, and Protein

Many
different kinds of intact proteins are being found in "ancient"
fossils that are not completely fossilized. Some scientists seem to have
found intact hemoglobin molecules in the bones of 65 million-year-old T. rex
fossils! How fairly large portions of such a seemingly delicate molecule
could survive intact over many millions of years is quite a mystery.

"The
lab filled with murmurs of amazement, for I had focused on something inside the
vessels that none of us had ever noticed before: tiny round objects, translucent
red with a dark center. Then a colleague took one look at them and shouted,
'You've got red blood cells. You've got red blood cells!'. It was exactly
like looking at a slice of modern bone.But, of course, I couldn’t
believe it. I said to the lab technician: 'The bones, after all, are 65 million
years old.How could blood cells survive that long?'" 13,14

This
account was given by Mary Schweitzer, a PhD student at the time, from Montana
State University. A well preserved Tyrannosaurus rex skeleton had
been found in 1990 and brought for analysis too Montana State University.
During microscopic examination of the fossilized remains, it was noted that some
portions of the long bones had not mineralized, but were in fact original bone.
Upon closer examination it was noted that within the vascular system of this
bone were what appeared to be red blood cells (note retained nucleus in the
center of the apparent RBCs and the fact that reptiles and bird generally retain
the RBC nucleus while mammals, like humans, do not). Of course, this did
not seem possible since the survival of intact red blood cells for some
65-million years seems very unlikely if not downright impossible.

Further
testing of these cells was done to attempt to disprove the notion that they
could possibly be red blood cells. Several analytical techniques were used
to characterize the material to include nuclear magnetic resonance (NMR), Raman
resonance and Raman spectroscopy (RR) and electron spin resonance (ESR).
These techniques did identify the presence of the heme group molecule,
but the detection limits of these methods were not able to rule-out or rule-in
the presence of hemoglobin or myoglobin proteins due to the small
amount of specimen available. So, Schweitzer and her team decided to
use a more sensitive detection method, the immune system. They injected
some of the T. rex extract into laboratory rats to see if these rats
would mount an immune response to the foreign T. rex material. And,
the rats did mount a very specific immune response against hemoglobin.
This immune response was not only against heme, but hemoglobin, and not just
hemoglobin in general, but against a certain type of hemoglobin.42
The reaction was strongest against pigeon and rabbit hemoglobin. There was
also a weak reaction against turkey hemoglobin, but there was no reaction
against snake hemoglobin. The specificity of these reactions were further
confirmed by the lack of reactivity with plant and sandstone extracts.

Consider
the conclusions that Schweitzer and her team made concerning these findings:

"The
production of antibodies specific for hemoglobin in two rats injected with
the trabecular extract is striking evidence for the presence of
hemoglobin-derived peptides in the bone extract. . . That the antisera did
not react with snake hemoglobin shows that the reactivity is specific and
not artifact. . . When considered as a whole, the results support the
hypothesis that heme prosthetic groups and hemoglobin fragments were
preserved in the tissues of the Late Cretaceous dinosaur skeleton." 16

These
results are quite interesting since they indicate a very specific immune
response, not just against hemoglobin, but certain types of hemoglobin
molecules. Note again that the antibodies formed did not react against snake
hemoglobin indicating that the antibody reactivity was "specific and not
artifact." The question is, how much of the original T. rex
hemoglobin molecule would need to be intact to elicit such a specific immune
response in the laboratory rats?

Schweitzer
goes on to suggest that "Immunogenicity is not dependent on fully intact
protein, and even very small peptides are immunogenic when complexed with larger
organic molecules . . . even after extensive degradation has occurred."42
But how extensively, roughly, could the hemoglobin molecules have degraded and
yet retain their ability to elicit a fairly strong and quite specific immune
reaction in laboratory rats? In order to obtain such strongly specific
immunogenicity it would seem that a significant percentage of the globin
portion of the hemoglobin molecule would need to be intact. But, how
could a protein of any significant size large enough to elicit such a specific
immune response be maintained over the course of 65 million years? One
might very reasonably conclude that natural decay, over this amount of time,
would completely destroy the ability of hemoglobin or the required larger
fragments of degraded hemoglobin from being antigenic in such a specific way.

The
explanation for this phenomenon, given later by Dr. Horner (Schweitzer's boss)
and even Schweitzer herself, was that the tougher heme molecule survived the 65
million years with maybe three or four amino acids of the original globin
molecules attached to it. Consider the following statement Schweitzer made
in a response to an inquiry by Jack Debaun:

"But
the heme itself is too small to be immunogenic [only about 652 daltons].
We believe that there were possibly 3-4 amino acids from the original
protein attached to the heme, and that was what may have spiked the immune
response." 17

Now,
it just seems quite unlikely that just 3 or 4 amino acids stuck onto a heme
group is going to give rise to an immune response as specific for a certain type
of hemoglobin as was found in this case (Note that a fully formed globin
molecule ranges from 141 to 146 amino acids in length with specific folding
characteristics that antibodies detect). As
far as I have been able to tell, the degree of immune response specificity noted
by Schweitzer et al. has never been realized in any confirming experiment with
so few hemoglobin amino acids stuck to a heme group and I doubt that such an
attempted experiment will ever be successful.

There
are several reasons why I feel this way.For
one thing, a certain minimum antigen size is required before it can
elicit an immune response. The most potent immunogens are macromolecular
proteins with molecular weights greater than 100,000da (~740aa - Note: the
average amino acid weighs ~135da).Substances
weighing less than 10,000da (~75aa) are only weakly immunogenic, and those
foreign proteins/antigens weighing less than 1,000da (~7aa) are usually
completely non-immunogenic. Homopolymers (repeats of the same amino acid) are
pretty much non-immunogenic regardless of size.Co-polymers of glutamic acid and lysine must be ~35,000da (~250aa) to be
immunogenic. It seems then that, in
general, immunogenicity increases with structural complexity.Also, aromatic amino acids, such as tyrosine or phenylalanine, contribute
much more to immunogenicity than do non-aromatic amino acids.For example, the addition of tyrosine to a co-polymer made up of
glutamate and lysine reduces the size limitation to ~15,000da (~100aa) and
adding tyrosine and phenylalanine together reduces the minimum to 4,000da
(~30aa).Also, it is all four
levels of protein structure (1o, 2o, 3o, &
4o) that influence immunogenicity - not just a short linear sequence
of amino acids.18-21

Of
course, a rather specific immune response can be elicited by relatively few
amino acids as part of an epitope on a larger protein molecule, but they usually
are not immunogenic without first being part of a larger molecule.Also, epitopes are not usually sequential in nature but are assembled by
protein folding.This means that a
rather large portion of the original molecule usually needs to be intact in
order for most epitopes to remain intact.Epitopes
with definite three-dimensional shapes and charged amino acids are particularly
well recognized by antibodies. The average epitope probably involves about 7 to
15 contact amino acid residues and a few of these may be critical to the
epitope's specificity and the avidity of the antibody-antigen reaction.18-21
But, in order to make an epitope antigenic, it must be processed first.

Antigen
presenting cells (APCs) like macrophages, dendritic cells, and even B-cells are
responsible for antigen processing and the presentation of epitopes/antigens to
the T-cells.T-cells do not
recognize the initial foreign antigen directly.They only recognize processed parts of antigens, consisting of no more
than 15 or so amino acids, presented to them by APCs in association with MHC
(major histocompatibility) molecules.So,
in order to activate T-cells (required for cellular immunity and very helpful in
humoral immunity), the foreign antigen must first be recognized as
"foreign" by the APC cells.This
initial APC recognition requires more than just a handful of amino acids
floating around or else there would be complete meltdown of the immune system.In fact, generally speaking, molecules with a molecular weight less than
10,000da (~75aa) are only weakly immunogenic when picked up by APC cells.Significant potency usually requires antigens to be rather
large at over 100,000da (~750aa).22,23

Given
all this, it seems quite difficult for me to imagine how "3 or 4"
amino acids stuck to a heme group could elicit an immune response that was so specific
for a certain type of hemoglobin. Recall
that the heme molecule, by itself, only has a molecular weight of around
652da.To make a strong as well as
specific immunogen (such as the strongly specific hemoglobin immunity developed
in rats exposed to T. rex extract in this case) one might expect the
immunogenic hemoglobin molecule to be at least 10,000da (~75aa or so) in size.18-21Certainly
then, a heme group with 3 or 4 amino acids attached to it (just over 1,000da)
would not seem to give rise to the relatively strong and specific immune
response (specific to a certain type of hemoglobin) observed by Schweitzer et
al. in rats exposed to T. rex bony extract.

However,
the argument is sometimes used that Schweitzer failed to identify any specific
size of hemoglobin fragment by gel electrophoresis. What happened is that
the electrophoretic pattern observed by Schweitzer when she ran the T. rex
proteins through the gel was a diffuse or smeared pattern. This means that
there were no discrete clusters of proteins that were the same size. But
this is only to be expected since a wide range of protein sizes would only be
expected after an extended period of degradation. The fact of the
matter is though that hemoglobin fragments ranging between 30 and 200 amino
acids in size where definitely present in the T. rex extract (per NMR analysis
filtering).16

Another
argument often used is that the molecules that elicited the immune response were
indeed quite large, but they were made up of fragments of smaller hemoglobin
molecules and other organic and inorganic molecules to form a new collective
molecule. The problem here is that there is that this hypothesis has not
been tested or demonstrated. Beyond this it doesn't seem very likely.
For one thing heme is non-covalently bonded to the globin portion of the
hemoglobin molecule. If the much stronger covalent bonds were broken and
rearranged so much between the remaining amino acids, how is it reasonable that
the relatively weak non-covalent bond between the amino acids and the heme group
would be maintained? Also, such rearrangement of covalent bonds would have
distorted the covalent bonds within the amino acids themselves as well as
between the covalent bonds they share with other amino acids. This level
of decay would alter the type of amino acids or destroy them as amino acids
completely. The specificity of the immune response against hemoglobin in
particular speaks strongly against this degree of change having taken place.

If
this is not already enough, Schweitzer recently made an even more startling
discovery. About three years ago (2002) she and her team had to divide a
very large T. rex thigh bone in order to transport it on a helicopter.
When the bone was opened flexible, even elastic, soft tissue "meat"
was found inside. This is incredible because this bone was supposed to be some
68 million years old. Microscopic examination revealed fine delicate
blood vessels with what appear to be intact red blood cells and other type of
cells like osteocytes - which are bone forming cells. These vessels were still
soft, translucent, and flexible.Subsequent
examination of other previously excavated T. rex bones from this and
other areas have also shown non-fossilized soft tissue preservation in most
instances.31

This
find calls into question not only the nature of the fossilization process, but
also the age of these fossils. How such soft tissue preservation and detail
could be realized after 68 million years is more than miraculous - - It is
unbelievable! Schweitzer herself comments that, "We may not really know as
much about how fossils are preserved as we think . . .” 31
Now, if that is not an understatement I'm not sure what is.

So,
it
seems rather clear, despite the objections of many evolutionists, to include
Schweitzer herself, that a 1,000da molecule would elicit an extremely weak
response at best and would not necessarily elicit a specific response to a
certain type of hemoglobin molecule since surface epitopes are generally more
specific in their antigenic nature than are buried epitopes (i.e., heme is
somewhat hidden within a cleft of the hemoglobin molecule so 3 or 4 amino acids
attached to it would also be somewhat hidden).How
then is it remotely logical to suggest that a molecule weighing just over
1,000da (a heme group plus 3 or 4 amino acids) could elicit such a strong as
well as specific immune response as Schweitzer et al. observed?
In light of the additional recent finds of even more striking soft tissue and
blood cell preservation, it
seems much more likely that such an immune response so specific for certain
types of hemoglobin could only be elicited by a larger portion of intact
hemoglobin than many scientists seem to even consider. Of course, one
can't really blame them because explaining how delicate soft tissue vessels
(with obvious red blood cells inside containing relatively large portions of
hemoglobin molecules) could remain intact for over 65 million years seems just a
little bit difficult.

Such
finds are much more consistent with a fairly recent catastrophic burial within
just a few thousand years of time. Non-catastrophic burial would allow for rapid
biodegradation of such delicate soft tissues. Time itself destroys soft tissues
as well as DNA and proteins in short order. Current real-time observations
suggest that bio-proteins could not remain intact more than a few tens of
thousands of years - 100,000 years at the very outside
limit of protein decay. The fact that such proteins are found, intact, in
bones supposedly older than 65 million years is simply inconsistent with such an
assumed age - by many orders of magnitude.

Carbon
14

I
think that one further study should be done.This study should be a Carbon
14 dating of this organic material as well as other “fossilized” organic
material. If any convincingly non-contaminant carbon 14 remains in any
detectable amount in organic specimens supposedly millions of years old, then a
real problem arises that is equivalent to finding a hominid in the Cambrian.
This, combined with the fresh DNA and protein problem seems to me to be quite a
quandary for the theory of evolution. At least I have not found a good
solution advocated in the scientific literature to explain these problems as of
late.